Princess Ubolratana was omitted from the official list of parties' candidates for prime minister.
The party's act, the election commission said, was "in opposition of the constitutional monarchy".
If found guilty, the party would be dissolved, and its board members banned from standing for political office.
The court is one of the most conservative institutions in Thailand and has consistently ruled in favor of the royalist point of view during political unrest over the past decade.
Party leader Preechaphol Pongpanit has said it did everything "sincerely, with good intentions", but added: "Above us is His Majesty and the monarchy". "But we're honest about what we've done". In several constituencies, Pheu Thai did not put up candidates in order to make way for Thai Raksa candidates, to increase their chances of a majority in parliament.
Thailand is scheduled to hold its general election on March 24. He is now running for the Phalang Pracharat party, a group aligned with the regime.
The changes were the latest attempt at quashing the influence of Thaksin, whose allied parties have won every national election since 2001 and remain popular with the rural majority for their populist policies such as universal health care.
It said in a statement that the Thai Raksa Chart Party had violated an electoral law with its nomination of the King's sister, which was "antagonistic towards the constitutional monarchy".
The announcement caused a sensation in a country where the royal family has traditionally remained above politics.
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The scuttling of her candidacy and potential moves to dissolve the Thai Raksa Chart party is a blow to the political machine of former premier Thaksin Shinawatra.
The royal family and electoral officials condemned her candidacy nearly immediately after it was announced.
In an Instagram post late on Tuesday, the 67-year-old apologised for her role in the drama.
"I'm sorry that the honest intention to work to help the country and our Thai people had caused problems that had seemed unlikely to occur in this day and age", Ubolratana wrote on Instagram, followed by the hashtag #howcomeitsthewayitis.
It was followed by the hashtag, in English, #howcomeitsthewayitis. Lawyers for the party said they will present their case before the constitution court, asking "for their mercy and justice".
Mr Pichit said that although the EC is empowered by law to seek Constitutional Court verdicts on alleged wrongdoings involving political parties, it could not do so without gathering sufficient evidence from the accused party. "We are confident in the fairness of the court and the judicial system".
The action against Thai Raksa Chart could strengthen both the pro-Thaksin and anti-Thaksin sides, said Titipol Phakdeewanich, a political science professor at Ubon Ratchathani University.
"If they don't let us tell our side, it'd be as if we were tied by our hands and feet", he said.
This is now bound to be a more heated election campaign.
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